../bin/calculate_SNP_error_rates.py                                                                                                                                                                                                                                                           					\
														--debug -vv --log_file logs/calculate_SNP_error_rates.log                                                                                                                                       		\
                                        -G "BAC callable"                                   			-g results/filter_snps/nod_from_bac.bac_final_callable/all.snps                                                                                                                                       		\
                                        -S 'short read callable NOD'                        			-s results/filter_snps/nod_from_vcf.bac_final_callable/all.snps                             		-r results/snp_calling_differences/bac_final_callable_vs_short_read_final_callable                                  	\
                                        -S 'short read callable NOD above threshold'        			-s results/filter_snps/nod_from_vcf.bac_final_callable.above_threshold/all.snps             		-r results/snp_calling_differences/bac_final_callable_vs_short_read_final_callable.above_threshold                  	\
                                        -S "Perlegen callable"                              			-s results/filter_snps/nod_from_perlegen.bac_final_callable/all.snps                        		-r results/snp_calling_differences/bac_final_callable_vs_perlegen_final_callable                                    	\
                                        -S "dbSNP callable"                                 			-s results/filter_snps/nod_from_dbsnp.bac_final_callable/all.snps                           		-r results/snp_calling_differences/bac_final_callable_vs_dbsnp_final_callable
../bin/calculate_SNP_error_rates.py                                                                                                                                                                                                                                                           			\
                                                                                            --debug -vv --log_file logs/calculate_SNP_error_rates.log                                                                                                                                         			\
                                        -G "BAC"                                            -g results/filter_snps/nod_from_bac.bac/all.snps                                                                                                                                                  			\
                                        -S "Perlegen"                                       -s results/filter_snps/nod_from_perlegen.bac/all.snps                                  -r results/snp_calling_differences/bac_vs_perlegen                                                         			\
                                        -S "Perlegen any strain"                            -s results/filter_snps/any_strain_perlegen.bac/all.snps                                -r results/snp_calling_differences/bac_vs_perlegen_any_strain                                                     		\
                                        -S "dbSNP"                                          -s results/filter_snps/nod_from_dbsnp.bac/all.snps                                     -r results/snp_calling_differences/bac_vs_dbsnp                                                            			


